R/ssnap_audit_output_specs.R
In md0u80c9/SSNAPStats: Stroke Sentinel National Audit Project (SSNAP) Statistics Calculations
#' Team and Patient 72hr Cohort Key Indicators
#'
#' This is a vector of audit measures describing the outputs for the
#' team and patient 72hr cohort key indicators.
#'
#' Internally it is used to create the team72hrKIs and patient72hrKIs
#' cohorts. It is exposed externally to allow customisation of the
#' output spec.
# * -----------------------------------------------------------------
# * aggregated_output_kis_72hrs (single create output) --------------
# * -----------------------------------------------------------------
aggregated_output_kis_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Domain 1 ========================================================
ssnap_measures[["ClockStartToBrainImagingMins"]], NULL, "Scanning", "median",
ssnap_measures[["BrainImagingGrouped"]], "Within1hr", "Scanning", "pct",
ssnap_measures[["BrainImagingGrouped"]], "Within12hrs", "Scanning", "pct",
# Domain 2 ========================================================
ssnap_measures[["ClockStartToFirstStrokeUnitMins"]], NULL, "Stroke Unit", "median",
ssnap_measures[["FirstSUWithin4hrs"]], NULL, "Stroke Unit", "pct",
# Domain 3 ========================================================
ssnap_measures[["Thrombolysis"]], "Yes", "Thrombolysis", "pct",
ssnap_measures[["tPAIfMeetsRCPCriteria"]], NULL, "Thrombolysis", "pct",
ssnap_measures[["ClockStartToThrombolysisMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["tPAAndSUIn4hrs"]], NULL, "Thrombolysis", "pct",
ssnap_measures[["tPAWithin1hr"]], NULL, "Thrombolysis", "pct",
# Domain 4 ========================================================
ssnap_measures[["StrokeConsultantReview"]], "Within24hrs", "Specialist Assessment", "pct",
ssnap_measures[["ClockStartToConsultantMins"]], NULL, "Specialist Assessment", "median",
ssnap_measures[["StrokeNurseReview"]], "Within24hrs", "Specialist Assessment", "pct",
ssnap_measures[["ClockStartToStrokeNurseMins"]], NULL, "Specialist Assessment", "median",
ssnap_measures[["SwallowScreenWithin4hrs"]], NULL, "Specialist Assessment", "pct",
ssnap_measures[["SpLangTherapistSwallowWithin72hrs"]], NULL, "Specialist Assessment", "pct",
# Domain 8 ========================================================
ssnap_measures[["OccTherApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToOTMins"]], NULL, "Multidisciplinary team", "median",
ssnap_measures[["PhysioApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToPTMins"]], NULL, "Multidisciplinary team", "median",
ssnap_measures[["SLTCommApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToSLTCommMins"]], NULL, "Multidisciplinary team", "median"
)
#' 72hr Audit Compliance Measures
#'
#' This is a vector of audit measures describing the outputs for
#' establishing SSNAP audit compliance. Audit compliance is applied
#' to both 72hr and post-72hr measures.
#'
#' Internally it is used to create the team72hrKIs and patient72hrKIs
#' cohorts. It is exposed externally to allow customisation of the
#' output spec.
# * -----------------------------------------------------------------
# * aggregated_output_ac_72hrs (single create output) ---------------
# * -----------------------------------------------------------------
aggregated_output_ac_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["NihssCompletion"]], "Complete", "NIHSS at arrival", "d_n_pct",
ssnap_measures[["Nihss24HrsKnown"]], NULL, "NIHSS 24h", "d_n_pct",
ssnap_measures[["ClockStartToRecordCreationHours"]], "Admission data entry", NULL, "median",
ssnap_measures[["EthnicityKnown"]], NULL, "72h measures", "pct",
ssnap_measures[["SwallowScreen4hrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SwallowScreen72hrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["OTAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["PTAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SLTCommAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SwallowAssessment72hrsComplete"]], "72h measures", NULL, "pct"
)
#' Casemix 72hr Cohort Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' look at casemix from the 72hrs Cohorts.
#'
#' Internally it is used to create the Casemix tab in the portfolio.
# * -----------------------------------------------------------------
# * aggregated_output_casemix_72hrs (single create output) ----------
# * -----------------------------------------------------------------
aggregated_output_casemix_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Gender ==========================================================
ssnap_measures[["Gender"]], NULL, "Gender", "d_n_pct",
# Age =============================================================
ssnap_measures[["AgeOver80"]], NULL, "Age", "d_n_pct",
# TODO the below give errors:
# Error in summarise_impl(.data, dots) :
# Evaluation error: `false` must be type integer, not logical.
# ssnap_measures[["FemaleAgeOver80"]], NULL, "quartiles",
# ssnap_measures[["MaleAgeOver80"]], NULL, "quartiles",
ssnap_measures[["AgeOnArrivalGrouped"]], NULL, "Age", "d_n_pct",
# Comorbidities ===================================================
ssnap_measures[["ComorbidityCount"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["CongestiveHeartFailure"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["Hypertension"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["Diabetes"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["PreviousStrokeTIA"]], NULL, "Comorbidities", "d_n_pct",
# Atrial fibrillation ============================================
ssnap_measures[["AtrialFibrillation"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFOnAntiplatelet"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFOnAnticoagulant"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFMeds"]], NULL, "Atrial fibrillation", "d_n_pct",
# Stroke type ====================================================
ssnap_measures[["StrokeType"]], NULL, "Stroke type", "d_n_pct",
# mRS before stroke ===============================================
ssnap_measures[["RankinBeforeStroke"]], NULL, "Modified Rankin score", "d_n_pct",
# NIHSS ===========================================================
ssnap_measures[["LOCArrival"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssCompletion"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssOnArrivalGrouped"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssOnArrival"]], NULL, "NIHSS", "quartiles",
# Palliative care =================================================
ssnap_measures[["EndOfLifeWithin72hrs"]], NULL, "Palliative care", "d_n_pct",
ssnap_measures[["EndOfLifePathway"]], NULL, "Palliative care", "d_n_pct",
ssnap_measures[["ClockStartToPalliativeCare72Hours"]], NULL, "Palliative care",
"quartiles",
ssnap_measures[["OnsetInHospital"]], NULL, "In hospital stroke",
"d_n_pct"
)
#' Portfolio 72hr Cohort Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the 72hr portfolio. This is a large dataset and so should
#' only be used for this purpose: it is quicker to create a custom
#' audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_72hrs (single create output) --------
# * -----------------------------------------------------------------
aggregated_output_portfolio_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Case mix ========================================================
ssnap_measures[["AgeOnArrival"]], NULL, "Casemix", "median",
ssnap_measures[["StrokeType"]], NULL, "Casemix", "pct",
ssnap_measures[["RankinBeforeStrokeGrouped"]], NULL, "Casemix", "pct",
ssnap_measures[["LOCArrivalGrouped"]], NULL, "Casemix", "pct",
ssnap_measures[["NihssOnArrival"]], NULL, "Casemix", "quartiles",
ssnap_measures[["EndOfLifeWithin72hrs"]], NULL, "Casemix", "pct",
# Onset of symptoms ===============================================
ssnap_measures[["OnsetDateAccuracy"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetTimeAccuracy"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetTimeKnown"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetToArrivalGrouped"]], NULL, "Onset of symptoms", "d_n_pct",
# Timings from onset ==============================================
ssnap_measures[["OnsetToArrivalTimeMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToFirstStrokeUnitMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToBrainImagingMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToThrombolysisMins"]], NULL, "Timings from onset", "quartiles",
# Arrival by ambulance ============================================
ssnap_measures[["ArrivalByAmbulance"]], NULL, "Ambulance", "d_n_pct",
# Day and time of arrival (TODO) ==================================
# Scanning ========================================================
ssnap_measures[["BrainImagingGrouped"]], NULL, "Scanning", "d_n_pct",
ssnap_measures[["ClockStartToBrainImagingMins"]], NULL, "Scanning", "quartiles",
# Admission to stroke unit ========================================
ssnap_measures[["WentToAStrokeUnit"]], NULL, "Admission to stroke unit", "d_n_pct",
ssnap_measures[["ClockStartToFirstStrokeUnitMins"]], NULL, "Admission to stroke unit", "quartiles",
ssnap_measures[["FirstWard"]], NULL, "Admission to stroke unit", "d_n_pct",
ssnap_measures[["FirstSUWithin4hrs"]], NULL, "Admission to stroke unit", "d_n_pct",
# TODO Out of hours and SU within 4 hrs.
# Stroke nurse ====================================================
ssnap_measures[["StrokeNurseReview"]], NULL, "Stroke nurse", "d_n_pct",
ssnap_measures[["ClockStartToStrokeNurseMins"]], NULL, "Stroke nurse", "quartiles",
# Stroke consultant ===============================================
ssnap_measures[["StrokeConsultantReview"]], NULL, "Stroke consultant", "d_n_pct",
ssnap_measures[["ClockStartToConsultantMins"]], NULL, "Stroke consultant", "quartiles",
# Occupational Therapy ============================================
ssnap_measures[["OccTherReviewGrouped"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["ClockStartToOTMins"]], NULL, "Occupational therapy", "quartiles",
ssnap_measures[["OccTherApplicability"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["OccTherApplicableWithin72hrs"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["OccTherApplicableWithin24hrs"]], NULL, "Occupational therapy", "d_n_pct",
# Physiotherapy ===================================================
ssnap_measures[["PhysioReviewGrouped"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["ClockStartToPTMins"]], NULL, "Physiotherapy", "quartiles",
ssnap_measures[["PhysioApplicability"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["PhysioApplicableWithin72hrs"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["PhysioApplicableWithin24hrs"]], NULL, "Physiotherapy", "d_n_pct",
# Speech and language therapy (communication) =====================
ssnap_measures[["SLTCommReviewGrouped"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["ClockStartToSLTCommMins"]], NULL, "Speech and language therapy", "quartiles",
ssnap_measures[["SLTCommApplicability"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["SLTCommApplicableWithin72hrs"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["SLTCommApplicableWithin24hrs"]], NULL, "Speech and language therapy", "d_n_pct",
# First 72hr bundle (TODO) ========================================
# Swallow screening ===============================================
ssnap_measures[["SwallowScreen4hrsGrouped"]], NULL, "Swallow screening", "d_n_pct",
ssnap_measures[["ClockStartToSwallowScreen4hrsMins"]], NULL, "Swallow screening", "quartiles",
ssnap_measures[["SwallowScreen4hrsApplicability"]], NULL, "Swallow screening", "d_n_pct",
ssnap_measures[["SwallowScreenWithin4hrs"]], NULL, "Swallow screening", "d_n_pct",
# create_output( # TODO this has an error on it
# ssnap_measures[["SwallowScreen72hrsGrouped"]],
# output_type = "d_n_pct")
# create_output(
# ssnap_measures[["ClockStartToSwallowScreen72hrsMins"]],
# output_type = "quartiles"),
# create_output(
# ssnap_measures[["SwallowScreen72hrsApplicability"]],
# output_type = "d_n_pct"),
# create_output(
# ssnap_measures[["SwallowScreenWithin72hrs"]],
# output_type = "d_n_pct"),
# Swallow assessment ==============================================
ssnap_measures[["ClockStartToSpLangTherapistSwallowMins"]], NULL, "Swallow assessment", "quartiles",
ssnap_measures[["SpLangTherapistSwallow72hrsGrouped"]], NULL, "Swallow assessment", "d_n_pct",
ssnap_measures[["SpLangTherapistSwallowApplicability"]], NULL, "Swallow assessment", "d_n_pct",
ssnap_measures[["SpLangTherapistSwallowWithin72hrs"]], NULL, "Swallow assessment", "d_n_pct",
# Thrombolysis ====================================================
ssnap_measures[["Thrombolysis"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["ClockStartToThrombolysisMins"]], NULL, "Thrombolysis", "quartiles",
ssnap_measures[["ThrombolysedOnsetToClockStartMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["ThrombolysedClockStartToBrainImagingMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["ThrombolysedBrainImagingToNeedleMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["EligibleFortPAByRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAIfMeetsRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAIfDoesntMeetRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["EligibleOrThrombolysed"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["EligibleExcludingNoButs"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAWithin1hr"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAAndSUIn4hrs"]], NULL, "Thrombolysis", "d_n_pct",
# Thrombolysis complications ======================================
ssnap_measures[["ThrombolysisComplications"]], NULL, "Thrombolysis complications", "d_n_pct",
ssnap_measures[["ThrombolysisComplicationsGrouped"]], NULL, "Thrombolysis complications", "d_n_pct",
# NIHSS following thrombolysis ====================================
ssnap_measures[["Nihss24HrsKnown"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["Nihss24hrsSeverity"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["ChangeInNIHSSAt24hrs"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["Nihss24hrsScoreChange"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
# Onset to arrival ================================================
ssnap_measures[["DaysOnsetToArrival"]], NULL, "Days onset to arrival", "d_n_pct",
# Thrombectomy ====================================================
ssnap_measures[["Thrombectomy"]], NULL, "Thrombectomy", "d_n_pct",
ssnap_measures[["OnsetToIAIPunctureMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["OnsetToIAICompletionMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["ClockStartToIAIPunctureMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["PunctureToDeploymentMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["PunctureToIAICompletionMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["Nihss24hrsAfterIAIKnown"]], NULL, "Thrombectomy", "d_n_pct"
)
#' Portfolio post-72hr Cohort 7Day Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the post-72hr portfolio, 7-day cohort. This is a large
#' dataset and so should only be used for this purpose: it is quicker
#' to create a custom audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_post72hrs_7day (single create output)
# * -----------------------------------------------------------------
aggregated_output_portfolio_post72hrs_7day <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Continence plan =================================================
ssnap_measures[["ContinencePlanGrouped"]], NULL, "Continence plan", "d_n_pct",
ssnap_measures[["ClockStartToContinencePlanHours"]], NULL, "Continence plan", "quartiles",
ssnap_measures[["ContinencePlanApplicability"]], NULL, "Continence plan", "d_n_pct",
ssnap_measures[["ContinencePlanIfApplicable"]], NULL, "Continence plan", "d_n_pct",
# Nutrition =======================================================
ssnap_measures[["NutritionalScreeningByDischarge"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionalScreeningHighRisk"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionSeenDietitian"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionalApplicability"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["SeenDietitianIfApplicable"]], NULL, "Nutrition", "d_n_pct",
# Level of consciousness ==========================================
ssnap_measures[["WorstLOCFirst7Days"]], NULL, "Level of consciousness", "d_n_pct",
# Urinary tract infection =========================================
ssnap_measures[["UrinaryTractInfection"]], NULL, "Urinary tract infection", "d_n_pct",
# PneumoniaAntibiotics ============================================
ssnap_measures[["PneumoniaAntibiotics"]], NULL, "Urinary tract infection", "d_n_pct"
# K7.1 and K7.2 are omitted because a median of a categorical variable
# makes no sense.
# K7.3 onwards also makes no sense given LOC can't worsen from the
# 'Worst in first 7 days'.
)
#' Portfolio post-72hr Cohort Discharge Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the post-72hr portfolio, discharge cohort. This is a large
#' dataset and so should only be used for this purpose: it is quicker
#' to create a custom audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_post72hrs_7day (single create output)
# * -----------------------------------------------------------------
aggregated_output_portfolio_post72hrs_discharge <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Continence plan =================================================
ssnap_measures[["ContinencePlanIfApplicableIn21Days"]], NULL, "Continence plan", "d_n_pct",
# Mood screen =====================================================
ssnap_measures[["MoodScreenGrouped"]], NULL, "Mood screen", "d_n_pct",
ssnap_measures[["MoodScreenApplicability"]], NULL, "Mood screen", "d_n_pct",
# TODO Lots missing here
# Cognition screen ================================================
ssnap_measures[["CognitiveScreenApplicability"]], NULL, "Mood screen", "d_n_pct",
# TODO Lots missing here
# Mood and cognition ==============================================
# TODO Lots missing here
# Occupational therapy ============================================
# ssnap_measures[["OccTherApplicable"]], NULL, "Occupational therapy", "d_n_pct",
)
#' Portfolio Discharge Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the 72hr portfolio. This is a large dataset and so should
#' only be used for this purpose: it is quicker to create a custom
#' audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_kis_discharge (single create output) ----------
# * -----------------------------------------------------------------
aggregated_output_kis_discharge <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 2 ========================================================
#TODO: 90% stay is returning NAs
# ssnap_measures[["StayOver90PCInStrokeUnit"]], NULL, "pct",
# Domain 9 ========================================================
ssnap_measures[["ContinencePlanIfApplicableIn21Days"]], NULL, "pct",
ssnap_measures[["CognitionAndMoodAssessed"]], NULL, "pct",
# Domain 10 =======================================================
ssnap_measures[["JointCarePlanning"]], NULL, "pct",
ssnap_measures[["DischargedWithESD"]], NULL, "pct",
ssnap_measures[["AFWithAnticoagulation"]], NULL, "pct",
ssnap_measures[["DischargeNamedContact"]], NULL, "pct"
)
#' Team post-72hr (all teams) Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the all teams post-72hr key indicators. This is used in
#' performance reporting.
# * -----------------------------------------------------------------
# * aggregated_output_kis_team_post72hrs ----------------------------
# * -----------------------------------------------------------------
aggregated_output_kis_team_post72hrs <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 5 ========================================================
ssnap_measures[["OccTherApplicable"]], NULL, "pct",
ssnap_measures[["PCOccTherDays"]], NULL, "median",
ssnap_measures[["OccTherMinutes"]], NULL, "median",
# Domain 6 ========================================================
ssnap_measures[["PhysioApplicable"]], NULL, "pct",
ssnap_measures[["PCPhysioDays"]], NULL, "median",
ssnap_measures[["PhysioMinutes"]], NULL, "median",
# Domain 7 ========================================================
ssnap_measures[["SpeechLangApplicable"]], NULL, "pct",
ssnap_measures[["PCSpeechLangDays"]], NULL, "median",
ssnap_measures[["SpeechLangMinutes"]], NULL, "median"
)
#' Patient post-72hr (all teams) Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the all patient post-72hr key indicators. This is used in
#' performance reporting.
# * -----------------------------------------------------------------
# * aggregated_output_kis_patient_post72hrs ----------------------------
# * -----------------------------------------------------------------
aggregated_output_kis_patient_post72hrs <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 5 ========================================================
ssnap_measures[["OccTherApplicable"]], NULL, "pct",
ssnap_measures[["PCOccTherDays"]], NULL, "median",
ssnap_measures[["OccTherMinutes"]], NULL, "median",
# Domain 6 ========================================================
ssnap_measures[["PhysioApplicable"]], NULL, "pct",
ssnap_measures[["PCPhysioDays"]], NULL, "median",
ssnap_measures[["PhysioMinutes"]], NULL, "median",
# Domain 7 ========================================================
ssnap_measures[["SpeechLangApplicable"]], NULL, "pct",
ssnap_measures[["PCSpeechLangDays"]], NULL, "median",
ssnap_measures[["SpeechLangMinutes"]], NULL, "median",
# Domain 10 =======================================================
ssnap_measures[["JointCarePlanning"]], NULL, "pct",
ssnap_measures[["DischargedWithESD"]], NULL, "pct",
ssnap_measures[["AFWithAnticoagulation"]], NULL, "pct",
ssnap_measures[["DischargeNamedContact"]], NULL, "pct"
)
aggregated_output_kis_critical_hour <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["BrainImagingGrouped"]], "Within1hr", "Critical1Hr", "d_n_pct",
ssnap_measures[["ClinicianAssessedWithin1hr"]], NULL, "Critical1Hr", "d_n_pct",
ssnap_measures[["tPACriticalHourStandardWithin1hr"]], NULL, "Critical1Hr", "d_n_pct"
)
ssnap_measures_tests <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["Gender"]], "Male", "Gender", "d_n_pct",
ssnap_measures[["AgeOver80"]], NULL, "Age", "d_n_pct",
ssnap_measures[["AgeOnArrivalGrouped"]], NULL, "Age", "d_n_pct"
)
#' @export
ssnap_output_specs <- list(
"Tests" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = ssnap_measures_tests),
"Team72HrCohortKIs" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_kis_72hrs),
"Patient72HrCohortKIs" = list(
"cohort" = "Patient72HrCohort",
"outputs_table" = aggregated_output_kis_72hrs),
"Team72HrCohortPortfolio" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_portfolio_72hrs),
"Patient72HrCohortPortfolio" = list(
"cohort" = "Patient72HrCohort",
"outputs_table" = aggregated_output_portfolio_72hrs),
"TeamCasemix" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_casemix_72hrs),
"TeamDischargeCohortKIs" = list(
"cohort" = "TeamDischargeCohort",
"outputs_table" = aggregated_output_kis_discharge),
# TODO the 7-day cohort is bugged so we have to fudge by using the
# Discharge cohort to test with for now and fix this later.
"TeamPost72hrsCohortPortfolio7Day" = list(
"cohort" = "Team7DayCohort",
"outputs_table" = aggregated_output_portfolio_post72hrs_7day),
"TeamPost72HrsAllTeamsCohortKIs" = list(
"cohort" = "TeamPost72HrsAllTeamsCohort",
"outputs_table" = aggregated_output_kis_team_post72hrs),
#TODO Pt post-7day cohort not yet defined
"PatientPost72HrsAllTeamsCohortKIs" = list(
"cohort" = "PatientPost72HrCohort",
"outputs_table" = aggregated_output_kis_patient_post72hrs),
"CriticalHourCohortKIs" = list(
"cohort" = "CriticalHourCohort",
"outputs_table" = aggregated_output_kis_critical_hour)
)
md0u80c9/SSNAPStats documentation built on Feb. 11, 2020, 11:43 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Team and Patient 72hr Cohort Key Indicators
#'
#' This is a vector of audit measures describing the outputs for the
#' team and patient 72hr cohort key indicators.
#'
#' Internally it is used to create the team72hrKIs and patient72hrKIs
#' cohorts. It is exposed externally to allow customisation of the
#' output spec.
# * -----------------------------------------------------------------
# * aggregated_output_kis_72hrs (single create output) --------------
# * -----------------------------------------------------------------
aggregated_output_kis_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Domain 1 ========================================================
ssnap_measures[["ClockStartToBrainImagingMins"]], NULL, "Scanning", "median",
ssnap_measures[["BrainImagingGrouped"]], "Within1hr", "Scanning", "pct",
ssnap_measures[["BrainImagingGrouped"]], "Within12hrs", "Scanning", "pct",
# Domain 2 ========================================================
ssnap_measures[["ClockStartToFirstStrokeUnitMins"]], NULL, "Stroke Unit", "median",
ssnap_measures[["FirstSUWithin4hrs"]], NULL, "Stroke Unit", "pct",
# Domain 3 ========================================================
ssnap_measures[["Thrombolysis"]], "Yes", "Thrombolysis", "pct",
ssnap_measures[["tPAIfMeetsRCPCriteria"]], NULL, "Thrombolysis", "pct",
ssnap_measures[["ClockStartToThrombolysisMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["tPAAndSUIn4hrs"]], NULL, "Thrombolysis", "pct",
ssnap_measures[["tPAWithin1hr"]], NULL, "Thrombolysis", "pct",
# Domain 4 ========================================================
ssnap_measures[["StrokeConsultantReview"]], "Within24hrs", "Specialist Assessment", "pct",
ssnap_measures[["ClockStartToConsultantMins"]], NULL, "Specialist Assessment", "median",
ssnap_measures[["StrokeNurseReview"]], "Within24hrs", "Specialist Assessment", "pct",
ssnap_measures[["ClockStartToStrokeNurseMins"]], NULL, "Specialist Assessment", "median",
ssnap_measures[["SwallowScreenWithin4hrs"]], NULL, "Specialist Assessment", "pct",
ssnap_measures[["SpLangTherapistSwallowWithin72hrs"]], NULL, "Specialist Assessment", "pct",
# Domain 8 ========================================================
ssnap_measures[["OccTherApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToOTMins"]], NULL, "Multidisciplinary team", "median",
ssnap_measures[["PhysioApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToPTMins"]], NULL, "Multidisciplinary team", "median",
ssnap_measures[["SLTCommApplicableWithin72hrs"]], NULL, "Multidisciplinary team", "pct",
ssnap_measures[["ClockStartToSLTCommMins"]], NULL, "Multidisciplinary team", "median"
)
#' 72hr Audit Compliance Measures
#'
#' This is a vector of audit measures describing the outputs for
#' establishing SSNAP audit compliance. Audit compliance is applied
#' to both 72hr and post-72hr measures.
#'
#' Internally it is used to create the team72hrKIs and patient72hrKIs
#' cohorts. It is exposed externally to allow customisation of the
#' output spec.
# * -----------------------------------------------------------------
# * aggregated_output_ac_72hrs (single create output) ---------------
# * -----------------------------------------------------------------
aggregated_output_ac_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["NihssCompletion"]], "Complete", "NIHSS at arrival", "d_n_pct",
ssnap_measures[["Nihss24HrsKnown"]], NULL, "NIHSS 24h", "d_n_pct",
ssnap_measures[["ClockStartToRecordCreationHours"]], "Admission data entry", NULL, "median",
ssnap_measures[["EthnicityKnown"]], NULL, "72h measures", "pct",
ssnap_measures[["SwallowScreen4hrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SwallowScreen72hrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["OTAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["PTAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SLTCommAssessment72HrsComplete"]], "72h measures", NULL, "pct",
ssnap_measures[["SwallowAssessment72hrsComplete"]], "72h measures", NULL, "pct"
)
#' Casemix 72hr Cohort Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' look at casemix from the 72hrs Cohorts.
#'
#' Internally it is used to create the Casemix tab in the portfolio.
# * -----------------------------------------------------------------
# * aggregated_output_casemix_72hrs (single create output) ----------
# * -----------------------------------------------------------------
aggregated_output_casemix_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Gender ==========================================================
ssnap_measures[["Gender"]], NULL, "Gender", "d_n_pct",
# Age =============================================================
ssnap_measures[["AgeOver80"]], NULL, "Age", "d_n_pct",
# TODO the below give errors:
# Error in summarise_impl(.data, dots) :
# Evaluation error: `false` must be type integer, not logical.
# ssnap_measures[["FemaleAgeOver80"]], NULL, "quartiles",
# ssnap_measures[["MaleAgeOver80"]], NULL, "quartiles",
ssnap_measures[["AgeOnArrivalGrouped"]], NULL, "Age", "d_n_pct",
# Comorbidities ===================================================
ssnap_measures[["ComorbidityCount"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["CongestiveHeartFailure"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["Hypertension"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["Diabetes"]], NULL, "Comorbidities", "d_n_pct",
ssnap_measures[["PreviousStrokeTIA"]], NULL, "Comorbidities", "d_n_pct",
# Atrial fibrillation ============================================
ssnap_measures[["AtrialFibrillation"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFOnAntiplatelet"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFOnAnticoagulant"]], NULL, "Atrial fibrillation", "d_n_pct",
ssnap_measures[["AFMeds"]], NULL, "Atrial fibrillation", "d_n_pct",
# Stroke type ====================================================
ssnap_measures[["StrokeType"]], NULL, "Stroke type", "d_n_pct",
# mRS before stroke ===============================================
ssnap_measures[["RankinBeforeStroke"]], NULL, "Modified Rankin score", "d_n_pct",
# NIHSS ===========================================================
ssnap_measures[["LOCArrival"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssCompletion"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssOnArrivalGrouped"]], NULL, "NIHSS", "d_n_pct",
ssnap_measures[["NihssOnArrival"]], NULL, "NIHSS", "quartiles",
# Palliative care =================================================
ssnap_measures[["EndOfLifeWithin72hrs"]], NULL, "Palliative care", "d_n_pct",
ssnap_measures[["EndOfLifePathway"]], NULL, "Palliative care", "d_n_pct",
ssnap_measures[["ClockStartToPalliativeCare72Hours"]], NULL, "Palliative care",
"quartiles",
ssnap_measures[["OnsetInHospital"]], NULL, "In hospital stroke",
"d_n_pct"
)
#' Portfolio 72hr Cohort Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the 72hr portfolio. This is a large dataset and so should
#' only be used for this purpose: it is quicker to create a custom
#' audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_72hrs (single create output) --------
# * -----------------------------------------------------------------
aggregated_output_portfolio_72hrs <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Case mix ========================================================
ssnap_measures[["AgeOnArrival"]], NULL, "Casemix", "median",
ssnap_measures[["StrokeType"]], NULL, "Casemix", "pct",
ssnap_measures[["RankinBeforeStrokeGrouped"]], NULL, "Casemix", "pct",
ssnap_measures[["LOCArrivalGrouped"]], NULL, "Casemix", "pct",
ssnap_measures[["NihssOnArrival"]], NULL, "Casemix", "quartiles",
ssnap_measures[["EndOfLifeWithin72hrs"]], NULL, "Casemix", "pct",
# Onset of symptoms ===============================================
ssnap_measures[["OnsetDateAccuracy"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetTimeAccuracy"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetTimeKnown"]], NULL, "Onset of symptoms", "d_n_pct",
ssnap_measures[["OnsetToArrivalGrouped"]], NULL, "Onset of symptoms", "d_n_pct",
# Timings from onset ==============================================
ssnap_measures[["OnsetToArrivalTimeMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToFirstStrokeUnitMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToBrainImagingMins"]], NULL, "Timings from onset", "quartiles",
ssnap_measures[["OnsetToThrombolysisMins"]], NULL, "Timings from onset", "quartiles",
# Arrival by ambulance ============================================
ssnap_measures[["ArrivalByAmbulance"]], NULL, "Ambulance", "d_n_pct",
# Day and time of arrival (TODO) ==================================
# Scanning ========================================================
ssnap_measures[["BrainImagingGrouped"]], NULL, "Scanning", "d_n_pct",
ssnap_measures[["ClockStartToBrainImagingMins"]], NULL, "Scanning", "quartiles",
# Admission to stroke unit ========================================
ssnap_measures[["WentToAStrokeUnit"]], NULL, "Admission to stroke unit", "d_n_pct",
ssnap_measures[["ClockStartToFirstStrokeUnitMins"]], NULL, "Admission to stroke unit", "quartiles",
ssnap_measures[["FirstWard"]], NULL, "Admission to stroke unit", "d_n_pct",
ssnap_measures[["FirstSUWithin4hrs"]], NULL, "Admission to stroke unit", "d_n_pct",
# TODO Out of hours and SU within 4 hrs.
# Stroke nurse ====================================================
ssnap_measures[["StrokeNurseReview"]], NULL, "Stroke nurse", "d_n_pct",
ssnap_measures[["ClockStartToStrokeNurseMins"]], NULL, "Stroke nurse", "quartiles",
# Stroke consultant ===============================================
ssnap_measures[["StrokeConsultantReview"]], NULL, "Stroke consultant", "d_n_pct",
ssnap_measures[["ClockStartToConsultantMins"]], NULL, "Stroke consultant", "quartiles",
# Occupational Therapy ============================================
ssnap_measures[["OccTherReviewGrouped"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["ClockStartToOTMins"]], NULL, "Occupational therapy", "quartiles",
ssnap_measures[["OccTherApplicability"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["OccTherApplicableWithin72hrs"]], NULL, "Occupational therapy", "d_n_pct",
ssnap_measures[["OccTherApplicableWithin24hrs"]], NULL, "Occupational therapy", "d_n_pct",
# Physiotherapy ===================================================
ssnap_measures[["PhysioReviewGrouped"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["ClockStartToPTMins"]], NULL, "Physiotherapy", "quartiles",
ssnap_measures[["PhysioApplicability"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["PhysioApplicableWithin72hrs"]], NULL, "Physiotherapy", "d_n_pct",
ssnap_measures[["PhysioApplicableWithin24hrs"]], NULL, "Physiotherapy", "d_n_pct",
# Speech and language therapy (communication) =====================
ssnap_measures[["SLTCommReviewGrouped"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["ClockStartToSLTCommMins"]], NULL, "Speech and language therapy", "quartiles",
ssnap_measures[["SLTCommApplicability"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["SLTCommApplicableWithin72hrs"]], NULL, "Speech and language therapy", "d_n_pct",
ssnap_measures[["SLTCommApplicableWithin24hrs"]], NULL, "Speech and language therapy", "d_n_pct",
# First 72hr bundle (TODO) ========================================
# Swallow screening ===============================================
ssnap_measures[["SwallowScreen4hrsGrouped"]], NULL, "Swallow screening", "d_n_pct",
ssnap_measures[["ClockStartToSwallowScreen4hrsMins"]], NULL, "Swallow screening", "quartiles",
ssnap_measures[["SwallowScreen4hrsApplicability"]], NULL, "Swallow screening", "d_n_pct",
ssnap_measures[["SwallowScreenWithin4hrs"]], NULL, "Swallow screening", "d_n_pct",
# create_output( # TODO this has an error on it
# ssnap_measures[["SwallowScreen72hrsGrouped"]],
# output_type = "d_n_pct")
# create_output(
# ssnap_measures[["ClockStartToSwallowScreen72hrsMins"]],
# output_type = "quartiles"),
# create_output(
# ssnap_measures[["SwallowScreen72hrsApplicability"]],
# output_type = "d_n_pct"),
# create_output(
# ssnap_measures[["SwallowScreenWithin72hrs"]],
# output_type = "d_n_pct"),
# Swallow assessment ==============================================
ssnap_measures[["ClockStartToSpLangTherapistSwallowMins"]], NULL, "Swallow assessment", "quartiles",
ssnap_measures[["SpLangTherapistSwallow72hrsGrouped"]], NULL, "Swallow assessment", "d_n_pct",
ssnap_measures[["SpLangTherapistSwallowApplicability"]], NULL, "Swallow assessment", "d_n_pct",
ssnap_measures[["SpLangTherapistSwallowWithin72hrs"]], NULL, "Swallow assessment", "d_n_pct",
# Thrombolysis ====================================================
ssnap_measures[["Thrombolysis"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["ClockStartToThrombolysisMins"]], NULL, "Thrombolysis", "quartiles",
ssnap_measures[["ThrombolysedOnsetToClockStartMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["ThrombolysedClockStartToBrainImagingMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["ThrombolysedBrainImagingToNeedleMins"]], NULL, "Thrombolysis", "median",
ssnap_measures[["EligibleFortPAByRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAIfMeetsRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAIfDoesntMeetRCPCriteria"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["EligibleOrThrombolysed"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["EligibleExcludingNoButs"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAWithin1hr"]], NULL, "Thrombolysis", "d_n_pct",
ssnap_measures[["tPAAndSUIn4hrs"]], NULL, "Thrombolysis", "d_n_pct",
# Thrombolysis complications ======================================
ssnap_measures[["ThrombolysisComplications"]], NULL, "Thrombolysis complications", "d_n_pct",
ssnap_measures[["ThrombolysisComplicationsGrouped"]], NULL, "Thrombolysis complications", "d_n_pct",
# NIHSS following thrombolysis ====================================
ssnap_measures[["Nihss24HrsKnown"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["Nihss24hrsSeverity"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["ChangeInNIHSSAt24hrs"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
ssnap_measures[["Nihss24hrsScoreChange"]], NULL, "NIHSS after thrombolysis", "d_n_pct",
# Onset to arrival ================================================
ssnap_measures[["DaysOnsetToArrival"]], NULL, "Days onset to arrival", "d_n_pct",
# Thrombectomy ====================================================
ssnap_measures[["Thrombectomy"]], NULL, "Thrombectomy", "d_n_pct",
ssnap_measures[["OnsetToIAIPunctureMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["OnsetToIAICompletionMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["ClockStartToIAIPunctureMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["PunctureToDeploymentMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["PunctureToIAICompletionMins"]], NULL, "Thrombectomy", "quartiles",
ssnap_measures[["Nihss24hrsAfterIAIKnown"]], NULL, "Thrombectomy", "d_n_pct"
)
#' Portfolio post-72hr Cohort 7Day Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the post-72hr portfolio, 7-day cohort. This is a large
#' dataset and so should only be used for this purpose: it is quicker
#' to create a custom audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_post72hrs_7day (single create output)
# * -----------------------------------------------------------------
aggregated_output_portfolio_post72hrs_7day <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Continence plan =================================================
ssnap_measures[["ContinencePlanGrouped"]], NULL, "Continence plan", "d_n_pct",
ssnap_measures[["ClockStartToContinencePlanHours"]], NULL, "Continence plan", "quartiles",
ssnap_measures[["ContinencePlanApplicability"]], NULL, "Continence plan", "d_n_pct",
ssnap_measures[["ContinencePlanIfApplicable"]], NULL, "Continence plan", "d_n_pct",
# Nutrition =======================================================
ssnap_measures[["NutritionalScreeningByDischarge"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionalScreeningHighRisk"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionSeenDietitian"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["NutritionalApplicability"]], NULL, "Nutrition", "d_n_pct",
ssnap_measures[["SeenDietitianIfApplicable"]], NULL, "Nutrition", "d_n_pct",
# Level of consciousness ==========================================
ssnap_measures[["WorstLOCFirst7Days"]], NULL, "Level of consciousness", "d_n_pct",
# Urinary tract infection =========================================
ssnap_measures[["UrinaryTractInfection"]], NULL, "Urinary tract infection", "d_n_pct",
# PneumoniaAntibiotics ============================================
ssnap_measures[["PneumoniaAntibiotics"]], NULL, "Urinary tract infection", "d_n_pct"
# K7.1 and K7.2 are omitted because a median of a categorical variable
# makes no sense.
# K7.3 onwards also makes no sense given LOC can't worsen from the
# 'Worst in first 7 days'.
)
#' Portfolio post-72hr Cohort Discharge Aggregation of Measures
#'
#' This is a vector of audit measures describing the measures used to
#' create the post-72hr portfolio, discharge cohort. This is a large
#' dataset and so should only be used for this purpose: it is quicker
#' to create a custom audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_portfolio_post72hrs_7day (single create output)
# * -----------------------------------------------------------------
aggregated_output_portfolio_post72hrs_discharge <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
# Continence plan =================================================
ssnap_measures[["ContinencePlanIfApplicableIn21Days"]], NULL, "Continence plan", "d_n_pct",
# Mood screen =====================================================
ssnap_measures[["MoodScreenGrouped"]], NULL, "Mood screen", "d_n_pct",
ssnap_measures[["MoodScreenApplicability"]], NULL, "Mood screen", "d_n_pct",
# TODO Lots missing here
# Cognition screen ================================================
ssnap_measures[["CognitiveScreenApplicability"]], NULL, "Mood screen", "d_n_pct",
# TODO Lots missing here
# Mood and cognition ==============================================
# TODO Lots missing here
# Occupational therapy ============================================
# ssnap_measures[["OccTherApplicable"]], NULL, "Occupational therapy", "d_n_pct",
)
#' Portfolio Discharge Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the 72hr portfolio. This is a large dataset and so should
#' only be used for this purpose: it is quicker to create a custom
#' audit spec for specific purposes.
# * -----------------------------------------------------------------
# * aggregated_output_kis_discharge (single create output) ----------
# * -----------------------------------------------------------------
aggregated_output_kis_discharge <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 2 ========================================================
#TODO: 90% stay is returning NAs
# ssnap_measures[["StayOver90PCInStrokeUnit"]], NULL, "pct",
# Domain 9 ========================================================
ssnap_measures[["ContinencePlanIfApplicableIn21Days"]], NULL, "pct",
ssnap_measures[["CognitionAndMoodAssessed"]], NULL, "pct",
# Domain 10 =======================================================
ssnap_measures[["JointCarePlanning"]], NULL, "pct",
ssnap_measures[["DischargedWithESD"]], NULL, "pct",
ssnap_measures[["AFWithAnticoagulation"]], NULL, "pct",
ssnap_measures[["DischargeNamedContact"]], NULL, "pct"
)
#' Team post-72hr (all teams) Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the all teams post-72hr key indicators. This is used in
#' performance reporting.
# * -----------------------------------------------------------------
# * aggregated_output_kis_team_post72hrs ----------------------------
# * -----------------------------------------------------------------
aggregated_output_kis_team_post72hrs <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 5 ========================================================
ssnap_measures[["OccTherApplicable"]], NULL, "pct",
ssnap_measures[["PCOccTherDays"]], NULL, "median",
ssnap_measures[["OccTherMinutes"]], NULL, "median",
# Domain 6 ========================================================
ssnap_measures[["PhysioApplicable"]], NULL, "pct",
ssnap_measures[["PCPhysioDays"]], NULL, "median",
ssnap_measures[["PhysioMinutes"]], NULL, "median",
# Domain 7 ========================================================
ssnap_measures[["SpeechLangApplicable"]], NULL, "pct",
ssnap_measures[["PCSpeechLangDays"]], NULL, "median",
ssnap_measures[["SpeechLangMinutes"]], NULL, "median"
)
#' Patient post-72hr (all teams) Cohort Key Indicators
#'
#' This is a vector of audit measures describing the measures used to
#' create the all patient post-72hr key indicators. This is used in
#' performance reporting.
# * -----------------------------------------------------------------
# * aggregated_output_kis_patient_post72hrs ----------------------------
# * -----------------------------------------------------------------
aggregated_output_kis_patient_post72hrs <- tibble::tribble(
~x, ~numerator, ~output_type,
# Domain 5 ========================================================
ssnap_measures[["OccTherApplicable"]], NULL, "pct",
ssnap_measures[["PCOccTherDays"]], NULL, "median",
ssnap_measures[["OccTherMinutes"]], NULL, "median",
# Domain 6 ========================================================
ssnap_measures[["PhysioApplicable"]], NULL, "pct",
ssnap_measures[["PCPhysioDays"]], NULL, "median",
ssnap_measures[["PhysioMinutes"]], NULL, "median",
# Domain 7 ========================================================
ssnap_measures[["SpeechLangApplicable"]], NULL, "pct",
ssnap_measures[["PCSpeechLangDays"]], NULL, "median",
ssnap_measures[["SpeechLangMinutes"]], NULL, "median",
# Domain 10 =======================================================
ssnap_measures[["JointCarePlanning"]], NULL, "pct",
ssnap_measures[["DischargedWithESD"]], NULL, "pct",
ssnap_measures[["AFWithAnticoagulation"]], NULL, "pct",
ssnap_measures[["DischargeNamedContact"]], NULL, "pct"
)
aggregated_output_kis_critical_hour <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["BrainImagingGrouped"]], "Within1hr", "Critical1Hr", "d_n_pct",
ssnap_measures[["ClinicianAssessedWithin1hr"]], NULL, "Critical1Hr", "d_n_pct",
ssnap_measures[["tPACriticalHourStandardWithin1hr"]], NULL, "Critical1Hr", "d_n_pct"
)
ssnap_measures_tests <- tibble::tribble(
~x, ~numerator, ~category, ~output_type,
ssnap_measures[["Gender"]], "Male", "Gender", "d_n_pct",
ssnap_measures[["AgeOver80"]], NULL, "Age", "d_n_pct",
ssnap_measures[["AgeOnArrivalGrouped"]], NULL, "Age", "d_n_pct"
)
#' @export
ssnap_output_specs <- list(
"Tests" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = ssnap_measures_tests),
"Team72HrCohortKIs" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_kis_72hrs),
"Patient72HrCohortKIs" = list(
"cohort" = "Patient72HrCohort",
"outputs_table" = aggregated_output_kis_72hrs),
"Team72HrCohortPortfolio" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_portfolio_72hrs),
"Patient72HrCohortPortfolio" = list(
"cohort" = "Patient72HrCohort",
"outputs_table" = aggregated_output_portfolio_72hrs),
"TeamCasemix" = list(
"cohort" = "Team72HrCohort",
"outputs_table" = aggregated_output_casemix_72hrs),
"TeamDischargeCohortKIs" = list(
"cohort" = "TeamDischargeCohort",
"outputs_table" = aggregated_output_kis_discharge),
# TODO the 7-day cohort is bugged so we have to fudge by using the
# Discharge cohort to test with for now and fix this later.
"TeamPost72hrsCohortPortfolio7Day" = list(
"cohort" = "Team7DayCohort",
"outputs_table" = aggregated_output_portfolio_post72hrs_7day),
"TeamPost72HrsAllTeamsCohortKIs" = list(
"cohort" = "TeamPost72HrsAllTeamsCohort",
"outputs_table" = aggregated_output_kis_team_post72hrs),
#TODO Pt post-7day cohort not yet defined
"PatientPost72HrsAllTeamsCohortKIs" = list(
"cohort" = "PatientPost72HrCohort",
"outputs_table" = aggregated_output_kis_patient_post72hrs),
"CriticalHourCohortKIs" = list(
"cohort" = "CriticalHourCohort",
"outputs_table" = aggregated_output_kis_critical_hour)
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.